Align PTS system, galactitol-specific, IIC component, component of Pentitol [arabitol (arabinitol, lyxitol)/xylitol] PTS permease, IICBA (encoded within an operon that also encodes a polyol-P dehydrogenase, a ribose-5-P isomerase, a ribulose 5-P-3-epimerase, and a BlgG-type PTS antiterminator) (Saklani-Jusforgues et al., 2001; Kentache T et al., 2016, in press) (characterized)
to candidate BWI76_RS14905 BWI76_RS14905 hypothetical protein
Query= TCDB::Q71WA6 (423 letters) >FitnessBrowser__Koxy:BWI76_RS14905 Length = 420 Score = 335 bits (858), Expect = 2e-96 Identities = 162/412 (39%), Positives = 265/412 (64%), Gaps = 3/412 (0%) Query: 8 VQYVLNLGPTVILPIMIFFIALIFRVPAKKALRSAITIGIGFVGINLVISLLSSNLGPAA 67 + +++LG +V++P++ F IAL F V A ++ + +GIGF G+ LVI LL +NLGPA+ Sbjct: 4 INSIISLGASVMMPVIFFIIALCFGVKVGTAFKAGMLVGIGFEGVGLVIGLLLTNLGPAS 63 Query: 68 QQMVERFGLNLTIIDAGWPAAAAASWASPVAAILIPICLVVNLALIFFKVTKTLDIDIWN 127 Q MVER GL+LT++D GWP A+ W SP+ ++ +V+N+A++ K+TKT++IDI+N Sbjct: 64 QAMVERIGLHLTVVDTGWPTASTIGWGSPLMLPVVVGFIVINIAMLLLKLTKTVNIDIFN 123 Query: 128 YWHFIAAGATGYIVTGGNWWFAILCAIIYEVAVLWMADRTQPMVEEFYGLKGISLPTGST 187 YW F+ G+ Y TG N+W ++ + L AD T P +++ Y L+GIS P + Sbjct: 124 YWIFLIMGSVVYAGTG-NYWLSVGITFGIFILTLLAADLTAPYLQKNYNLQGISFPHLTC 182 Query: 188 AAFGFIGIPVGWLIAKIPGIKNIHVDPETIQKRFGIFGEPMMMGLILGIAIGILAGYDVG 247 + GI ++I KIP I I+ DPE+I K+FG+FGEP+ +G +LG+ + LAGYDV Sbjct: 183 ITYVPFGIACNYIIDKIPLINKINFDPESINKKFGVFGEPLTLGFVLGLLLAFLAGYDVS 242 Query: 248 AVAQLGMSMGAVMFLMPRMVKILMEGLIPISESAREFMKSRFKGRELYIGLDAALSIGHP 307 A L + + A M L+P+M++IL++GL+ + ++A +K++F R+ YIG+D AL IG P Sbjct: 243 AAVSLAIKVSAAMLLLPKMIEILVQGLLIVRDAAEAKLKAKFPDRDFYIGMDTALLIGEP 302 Query: 308 ANISTGLILVPITLFLAVIIPGNKVLPFGDLATIPFYVSFVVASRKGNILHSVLAGTVVI 367 + ++TGL+L+P+ + LA+I+PGN+VLPF DLA++ F ++ V K N+ + GT+V+ Sbjct: 303 SVLATGLLLIPMAVVLAIILPGNRVLPFVDLASLMFLLAMVTPFCKRNMFRMFITGTLVV 362 Query: 368 ALALLMATDFGLVHTE-MMKGVYEFPKGATQVSTLDMGGNF-FNWVILKFSQ 417 + L + TD +T+ + P+G ++++ + G W+ LKF + Sbjct: 363 SCILYVGTDISHEYTQAAVNSHIPVPEGMSEITNIVGGATTPVGWLALKFGE 414 Lambda K H 0.328 0.143 0.441 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 511 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 423 Length of database: 420 Length adjustment: 32 Effective length of query: 391 Effective length of database: 388 Effective search space: 151708 Effective search space used: 151708 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory